LOCUS       NZ_CP054579             2276 bp    DNA     circular CON 12-SEP-2023
DEFINITION  Staphylococcus saprophyticus strain UTI-050 plasmid pUTI-050-5,
            complete sequence.
ACCESSION   NZ_CP054579
VERSION     NZ_CP054579.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15089828
            Assembly: GCF_013343055.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus saprophyticus
  ORGANISM  Staphylococcus saprophyticus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2276)
  AUTHORS   Stephens,C., Wright,M., Hartman,A., Gonzales,A., Sensabaugh,G.,
            Robinson,P., Lopez,G. and Hess,D.
  TITLE     Complete genome sequences of diverse uropathogenic Staphylococcus
            saprophyticus isolates from a college health center
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2276)
  AUTHORS   Stephens,C., Wright,M., Hartman,A., Gonzales,A., Sensabaugh,G.,
            Robinson,P., Lopez,G. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-JUN-2020) Biology, Santa Clara University, 500 El
            Camino Real, Santa Clara, CA 95054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 168x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/12/2023 03:38:08
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,706
            CDSs (total)                      :: 2,621
            Genes (coding)                    :: 2,541
            CDSs (with protein)               :: 2,541
            Genes (RNA)                       :: 85
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 62
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 80
            CDSs (without protein)            :: 80
            Pseudo Genes (ambiguous residues) :: 0 of 80
            Pseudo Genes (frameshifted)       :: 42 of 80
            Pseudo Genes (incomplete)         :: 33 of 80
            Pseudo Genes (internal stop)      :: 23 of 80
            Pseudo Genes (multiple problems)  :: 16 of 80
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054579.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..2276
                     /organism="Staphylococcus saprophyticus"
                     /mol_type="genomic DNA"
                     /strain="UTI-050"
                     /isolation_source="urine specimens"
                     /host="Homo sapiens"
                     /db_xref="taxon:29385"
                     /plasmid="pUTI-050-5"
                     /geo_loc_name="USA: California"
                     /collection_date="2019"
     gene            join(2066..2276,1..794)
                     /locus_tag="HSZ50_RS13450"
                     /old_locus_tag="HSZ50_13470"
     CDS             join(2066..2276,1..794)
                     /locus_tag="HSZ50_RS13450"
                     /old_locus_tag="HSZ50_13470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020368559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001199882.1"
                     /translation="MQYNTTRCIDENQDNETLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EEVVKEKPKARWLFLTLSTKNAIDGDTLEQSLKHLTKAFDRLSRYKKVKQNLVGFLRST
                     EVTVNKNDGSYNQHMHVLLCVENSYFKNKANYITQEEWVNLWQKALQVNYRPVANIKAI
                     KPNQKGDKDIQAAIKETSKYSVKSSDFLTDDDERNQEIVNDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSITAIWNFEKQNYYLKDLKR"
                     /name="protein rep"
     gene            complement(1421..1744)
                     /gene="qacC"
                     /locus_tag="HSZ50_RS13455"
                     /old_locus_tag="HSZ50_13475"
     ARG             complement(1425..1744)
                     /name="qacC"
                     /gene="qacC"
                     /gene_name="quaternary ammonium compound efflux SMR
                     transporter QacC"
                     /tool="amrfinderplus"
                     /drug_class="QUATERNARY AMMONIUM"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(1422..1744)
                     /name="qacJ"
                     /gene="qacJ"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="71.96"
                     /coverage="100.0"
     Typing          2..794
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atttgaagtt acataagaca tggttttgta agtcgaaact ctgcccagtt tgtaattgga
       61 ggcgtgctat gaaaaatagt tatcaagctc aaaaagtgat tgaagaagtt gttaaagaaa
      121 aaccaaaagc gcgttggtta tttttaacac tttcaacgaa aaatgcgata gatggggata
      181 ctttagaaca aagtttgaaa catttaacga aagcatttga taggttaagt agatataaaa
      241 aagtgaagca aaatcttgtt gggtttttgc gttcaacgga agtaacagtt aataaaaatg
      301 atggtagtta taatcaacat atgcatgttt tattatgtgt tgaaaatagt tattttaaga
      361 ataaagctaa ttatataact caagaagaat gggttaattt atggcaaaaa gcattacaag
      421 taaattatcg acccgtagca aatattaaag cgatcaaacc aaatcaaaaa ggcgataaag
      481 atattcaagc agctatcaaa gaaacctcta aatattcggt taagtcatct gattttttaa
      541 ctgatgatga tgaaagaaat caagaaatcg tgaatgattt agaaaaaggt ttatatcgaa
      601 aacgtatgtt gagttatggt ggtttgctta aacaaaaaca taagatttta aatttagatg
      661 atgccgaaga tggcaatttg attaatacaa gtgacgaaga taaaacaaca gacgaagaag
      721 aaaaagcaca ttcaattacg gcaatttgga attttgaaaa acaaaattat tatttaaaag
      781 atttgaaacg ttagctaaaa agctagcgtt tttttatgtc tttttgcccc tgcgggaact
      841 atagcgttca accggcatgg ttgaccagtt ttcatgttaa cttttaagtt tgcatgtaaa
      901 tgggcagtgt ttattttttt ctgcccagtt tgctaaattt ttaatttgca tataactggg
      961 cagtgtctaa aaaattagtc actggttttg ctcaaatttt tgtttgtgaa attaagatat
     1021 atttatttgg ctcatatttg cgttttaaaa gcgtatatag acttttaggt ataaaactat
     1081 atgatttacc cctgaatctt taaaatgccc ccttaaaatt caaataaagg catataaaaa
     1141 taaaaagcca acccagataa aatggattgg ctttttattt gcttttgcga agtagattat
     1201 aaaaaactac ttttaataag caccctaaat gtgatgtcta tattataaca agaacacgca
     1261 tttatgccga gaaaatttat tgtgcgttga gaagaaccct taactaaact tgcagacgaa
     1321 tgtcggcata gcgtgagcta ttaagccgac cattcgacaa gttttgggat tgttaagggt
     1381 tccgaggctc aacgtcaata aagcaattgg aataaagcaa ttaatgcgat gttccgaaaa
     1441 tgtttaacga aactacgccg actatgatta aaactataga tactatagtt attagattta
     1501 tttgttcttt gaaaataatt attgagacta cggttgttaa gactaaacct agtcccgccc
     1561 aagttgcata agttatattt agtggtaggt gttgcattgt tttacttaaa aaatagaaac
     1621 aaattccaaa tgaaattatt gttcctaagg atggtataaa ttttgaaaag ccttctgaag
     1681 atttaagaaa tgcacttcca ataacttcag tacttatggc tattattaaa taaatataag
     1741 gcatttttaa ctccttttaa ttttcgtatt ttatttaatt ttattctaag tattttttaa
     1801 ttgtagtctt gtattttgag tgtcattcgc gtggtatttt tgtggattga tggtttttga
     1861 aaggtttttg aaacgagttg aaaacgagtt tcttcttgtc ttgatactat atagaaataa
     1921 ctcgatttta aaattatagc tgtaatcctt ggtatgtaag ggattatagc tatttttctt
     1981 gttgaaagga atttttgaca taaaaaaacc ccagtagtat gattaaagcg tctactcaat
     2041 aaacaactac tggaggtctc tttatatgca atataatact actagatgta tagacgaaaa
     2101 tcaagataac gaaacactta aagatatgac gaaaagtggg aaacaacgcc catggagaga
     2161 aaagaagata gataatgtaa gttatgcaga tatactggaa attttaaaaa taaaaaaggc
     2221 ttttaatgta aaacaatgtg gtaacgtctt agagttcaag ccgactgatg aaggtt
//
